RNA editing in bacteria: occurrence, regulation and significance

Abstract

DNA harbors the blueprint for life. However, the instructions stored in the DNA could be altered at the RNA level before they are executed. One of these processes is RNA editing, which was shown to modify RNA sequences in many organisms. The most abundant modification is the deamination of adenosine (A) into inosine (I). In turn, inosine can be identified as a guanosine (G) by the ribosome and other cellular machineries such as reverse transcriptase. In multicellular organisms, enzymes from the ADAR (adenosine deaminase acting on RNA) family mediate RNA editing in mRNA, whereas enzymes from the ADAT family mediate A-to-I editing on tRNAs. In bacteria however, until recently, only one editing site was described, in tRNA^Arg, but never in mRNA. The tRNA site was shown to be modified by tadA (tRNA specific adenosine deaminase) which is believed to be the ancestral enzyme for the RNA editing family of enzymes. In our recent work, we have shown for the first time, editing on multiple sites in bacterial mRNAs and identified tadA as the enzyme responsible for this editing activity. Focusing on one of the identified targets - the self-killing toxin hokB, we found that editing is physiologically regulated and that it increases protein activity. Here we discuss possible modes of regulation on hokB editing, potential roles of RNA editing in bacteria, possible implications, and future research directions.

Keywords: ADAR; ADAT; RNA editing; antibiotic tolerance; bacteria; hokB; non-genetic variation; persistence; tadA; toxin-antitoxin.

Figure 1.

Hypothesized RNA editing regulation in bacteria. In lag and early log phase tRNA^Arg is abundant and therefore limits the available tadA units for hokB mRNA editing. As cell density increase (i.e., approaching to stationary phase), tRNAs are found in lower numbers, freeing tadA units to edit additional copies of hokB mRNA (as well as other mRNAs), making the toxin more effective (by recoding a tyrosine codon into a cysteine, presumably allowing the generation of an S-S bond), thus contributing to hokB mediated antibiotic tolerance. This scenario can be accompanied with different affinities of tadA to its tRNA^Arg/mRNA substrates (lower Kd = higher affinity). In parallel hokB expression is also elevated upon approaching stationary phase further increasing hokB activity and antibiotic tolerance. The tRNA and hokB predicted structures are as shown in our original paper [15] and were predicted using the Vienna RNA Websuite [21] and RaptorX [22].

Figure 2.

RNA editing in bacteria can diversify the transcriptome and contribute to ‘non-genetic’ cell to cell variability. RNA editing (marked here as a red dot) can be found in similar levels in bacterial cells (affecting some or all hokB transcripts within each cell term here ‘within cell variability’). Alternatively, it could differ from cell to cell (term here ‘cell to cell variability’), thus contributing a second level of variability (the first being hokB transcription). Such a scenario can produce different sub-populations of cells expressing hokB with different editing levels that will respond differently to antibiotics (i.e, RNA editing dependent ‘bet hedging’). Because RNA is extracted from populations of bacteria, both scenarios shown here, will display editing level of 50%.